I've notice when you create multiple waypoints that go in a straight line for example:
1.) ATTACK 2.) DROP_ORD 3.) ATTACK
Which could represent a flight of bombers to drop on a target, that the flight starts acting very strange.
When you use the 'run mission' and look at the white cross the planes chase along each waypoint it will disappear and start again at the being of the DROP_ORD segment causing the planes to either circle back or wiggle back and forth while dropping altitude.
The problem goes away if you put a small direction change between each way point...